Molecular Breeding

, Volume 19, Issue 4, pp 291–296 | Cite as

Functional markers for xa5-mediated resistance in rice (Oryza sativa, L.)

  • Anjali S. Iyer-Pascuzzi
  • Susan R. McCouch


The recent cloning of several agronomically important genes has facilitated the development of functional markers. These markers reside within the target genes themselves and can be used with great reliability and efficiency to identify favorable alleles in a breeding program. Bacterial blight (BB) is a severe rice disease throughout the world that is controlled primarily through use of resistant cultivars. xa5 is a race-specific, recessive gene mediating resistance to BB. It is widely used in rice breeding programs throughout the tropics. Due to its recessive nature, phenotypic selection for xa5-mediated resistance is both slow and costly. Previously, marker assisted selection (MAS) for this resistance gene was not efficient because it involved markers that were only indirectly linked to xa5 and ran the risk of being separated from the trait by recombination. Recently, the cloning of the gene underlying this trait made it possible to develop functional markers. Here we present a set of CAPS markers for easy, quick and direct identification of cultivars or progeny carrying xa5-mediated resistance and provide evidence that these markers are 100% predictive of the presence of the xa5 allele. These markers are expected to enhance the reliability and cost-effectiveness of MAS for xa5-mediated resistance.


Bacterial blight Disease resistance Functional marker Plant improvement Marker assisted selection 



We thank Lois Swales for help with graphics and manuscript formatting. This work was supported by a USDA National Needs Fellowship in Molecular Plant Pathology no. 91-38420-6081 to AI-P and USDA NRI grant no. 2003-35301-13130.


  1. Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560PubMedCrossRefGoogle Scholar
  2. Blair MW, Garris AJ, Iyer AS, Chapman B, Kresovich S, McCouch SR (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107:62–73PubMedCrossRefGoogle Scholar
  3. Dubcovsky J (2004) Marker-assisted selection in public breeding programs: the wheat experience. Crop Sci 44:1895–1898CrossRefGoogle Scholar
  4. Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769PubMedGoogle Scholar
  5. Gnanamanickam S, Pryiyadarasani V, Narayanan N, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for management. Curr Sci 77:1435–1444Google Scholar
  6. Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354PubMedGoogle Scholar
  7. Jia Y, Wang Z, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149CrossRefGoogle Scholar
  8. Jiang GH, Xia ZH, Zhou YL, Wan J, Li DY, Chen RS, Zhai WX, Zhu LH (2006) Testifying the rice bacterial blight resistance gene xa5 by genetic complementation and further analyzing xa5 (Xa5) in comparison with its homolog TFIIAgamma1. Mol Genet Genomics 275:354–366PubMedCrossRefGoogle Scholar
  9. Kauffman HE, Reddy APD, Ksiek SPV, Marca SD (1973) An improved technique for evaluating resistance of race varieties to Xanthomonas oryzae. Plant Disease Reporter 57:537–541Google Scholar
  10. Koebner RM, Summers RW (2003) 21st century wheat breeding: plot selection or plate detection? Trends Biotechnol 21:59–63PubMedCrossRefGoogle Scholar
  11. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410PubMedCrossRefGoogle Scholar
  12. Ogawa T, Yamamoto T, Khush GS, Mew TW, Kaku H (1988) Near-isogenic lines as international differentials for resistance to bacterial blight of rice. Rice Genet Newslett 5:106–109Google Scholar
  13. Olufowote JO, Xu YB, Chen XL, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L) using microsatellite and RFLP markers. Genome 40:370–378PubMedGoogle Scholar
  14. Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal HS, Khush GS (2001) Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor Appl Genet 102:1011–1015CrossRefGoogle Scholar
  15. Toenniessen GH, O’Toole JC, DeVries J (2003) Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198PubMedCrossRefGoogle Scholar
  16. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630PubMedCrossRefGoogle Scholar
  17. Yamanaka S, Nakamura I, Watanabe KN, Sato YI (2004) Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet 108:1200–1204PubMedCrossRefGoogle Scholar
  18. Yoshimura S, Yoshimura A, Iwata N, McCouch SR, Abenes ML, Baraoidan MR, Mew TW, Nelson RJ (1995) Tagging and combining bacterial-blight resistance genes in rice using RAPD and RFLP markers. Mol Breed 1:375–387CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  2. 2.IthacaUSA

Personalised recommendations